Traits

Traits linked to HOXD13

homeobox D13

The Human Phenotype Ontology links 103 traits to HOXD13, by body system: features seen in people with one of the gene's rare conditions.

Abnormality of limbs

Trait	How often it is seen
Absent distal interphalangeal creases	Always
Absent middle bone of the 3rd toe	Always
Finger bends toward pinky	Very often (80–99%)
Fused 4th-5th long bones of hand	Very often (80–99%)
Fused long bones of hand	Very often (80–99%)
Fused toes	Very often (80–99%)
Fusion of the long bones of the feet	Very often (80–99%)
Short 5th long bone of foot	Very often (80–99%)
Short middle bone of index finger	Very often (80–99%)
Short middle bone of the little finger	Very often (80–99%)
Short outermost finger bone	Very often (80–99%)
Shortened 5th long bone of hand	Very often (80–99%)
Shortened long bone of hand	Very often (80–99%)
Type E brachydactyly	Very often (80–99%)
Ulnar deviation of the 2nd finger	Very often (80–99%)
Ulnar deviation of the 3rd finger	Very often (80–99%)
Ulnar deviation of the 4th finger	Very often (80–99%)
Ulnar deviation of the 5th finger	Very often (80–99%)
Webbed skin of 2nd-3rd toes	Very often (80–99%)
3-4 finger cutaneous syndactyly	Often (30–79%)
Aplasia/Hypoplasia of the radius	Often (30–79%)
Broad outermost bone of the thumb	Often (30–79%)
Bunion	Often (30–79%)
Fused finger bones	Often (30–79%)
Permanent flexion of the finger	Often (30–79%)
Shortened 4th long bone of hand	Often (30–79%)
Webbed 2nd and 3rd toes	Often (30–79%)
Webbed 3rd-4th fingers	Often (30–79%)
Webbed 4th-5th toes	Often (30–79%)
Absent/small outermost big toe bone	Sometimes (5–29%)
Curvature of little finger	Sometimes (5–29%)
Extra little finger	Sometimes (5–29%)
Extra thumb	Sometimes (5–29%)
Finger syndactyly	Sometimes (5–29%)
Preaxial foot polydactyly	Sometimes (5–29%)
Short long bone of foot	Sometimes (5–29%)
Unequal size of arms	Sometimes (5–29%)
Webbed 3rd-4th toes	Sometimes (5–29%)
6 long bones of hand	Not recorded
Broad big toe	Not recorded
Broad outermost bone of big toe	Not recorded
Contracture of the proximal interphalangeal joint of the 5th finger	Not recorded
Enlarged innermost hinge joint	Not recorded
Extra toe attached near the little toe	Not recorded
Fused wrist bones	Not recorded
Joint contracture of the hand	Not recorded
Mesoaxial hand polydactyly	Not recorded
Oligodactyly	Not recorded
Short digit	Not recorded
Short finger bones	Not recorded
Short fingers or toes	Not recorded
Type D brachydactyly	Not recorded
Underdeveloped 2nd-5th middle toe bones	Not recorded
Webbed fingers or toes	Not recorded
Y-shaped long bone of hand	Not recorded

Abnormality of the genitourinary system

Trait	How often it is seen
Abnormal kidney location	Often (30–79%)
Absent kidney	Often (30–79%)
Abnormal morphology of female internal genitalia	Sometimes (5–29%)
Ambiguous external genitalia	Sometimes (5–29%)
Cleft of scrotum	Sometimes (5–29%)
Hydronephrosis	Sometimes (5–29%)
Hypospadias	Sometimes (5–29%)
Multicystic kidney dysplasia	Sometimes (5–29%)
Underdeveloped penis	Sometimes (5–29%)
Undescended testes	Sometimes (5–29%)
Urethra issue	Sometimes (5–29%)

Abnormality of the musculoskeletal system

Trait	How often it is seen
Congenital diaphragmatic hernia	Often (30–79%)
Double-Jointed	Often (30–79%)
Vertebral segmentation defect	Often (30–79%)
Abnormal intervertebral disk morphology	Sometimes (5–29%)
Abnormal sacrum morphology	Sometimes (5–29%)
Abnormality of the ribs	Sometimes (5–29%)
Permanent flexion of the finger or toe	Not recorded
Short collarbone	Not recorded
Straight collarbone	Not recorded

Abnormality of head or neck

Trait	How often it is seen
Big calvaria	Sometimes (5–29%)
Brain tissue sticks out through back of skull	Sometimes (5–29%)
Cleft palate	Sometimes (5–29%)
Frontal bossing	Sometimes (5–29%)
Non-midline cleft of the upper lip	Sometimes (5–29%)
Wide fontanelles	Sometimes (5–29%)
Multiple impacted teeth	Not recorded
Round face	Not recorded

Abnormality of the digestive system

Trait	How often it is seen
Absent anus	Very often (80–99%)
Abnormal connection between trachea and esophagus	Often (30–79%)
Abnormality of the gallbladder	Sometimes (5–29%)
Abnormality of the pancreas	Sometimes (5–29%)
Anorectal anomaly	Sometimes (5–29%)
Omphalocele	Sometimes (5–29%)

Abnormality of prenatal development or birth

Trait	How often it is seen
High levels of amniotic fluid	Very often (80–99%)
Premature birth	Very often (80–99%)
Only one artery in umbilical cord instead of two	Sometimes (5–29%)

Abnormality of the cardiovascular system

Trait	How often it is seen
Abnormal cardiac septum morphology	Often (30–79%)
Abnormal cardiovascular system morphology	Often (30–79%)
Collection of dilated blood vessels that forms mass	Sometimes (5–29%)

Abnormality of the respiratory system

Trait	How often it is seen
Absent/small lungs	Very often (80–99%)
Narrowing of windpipe	Very often (80–99%)
Softening of voice box tissue	Often (30–79%)

Growth abnormality

Trait	How often it is seen
Short stature	Often (30–79%)
Prenatal growth deficiency	Sometimes (5–29%)
Moderate short stature	Not recorded

Abnormality of the ear

Trait	How often it is seen
Ears rotated toward back of head	Sometimes (5–29%)

Abnormality of the nervous system

Trait	How often it is seen
Anencephaly	Sometimes (5–29%)

How often is among people with one of the gene's conditions, the most often across them, as the Human Phenotype Ontology records it. These pages describe traits and the research behind them; they are not a diagnosis, and a doctor or genetic counsellor is the person to ask about symptoms.

Where this comes from

The Human Phenotype Ontology, release 2026-09-01: the traits linked to HOXD13 and how often each is seen. Find out more at hpo.jax.org.

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