DPH1 p.Pro332=

Q: Is DPH1 p.Pro332= (c.996T>C) pathogenic?

DPH1 p.Pro332= (c.996T>C) is classified Benign in DPH1 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2021-07-14). Common (popmax 93.8%, eas) — too common for a highly-penetrant pathogenic allele; Associated with developmental delay with short stature, dysmorphic facial features, and sparse hair.

Q: What condition is associated with DPH1 p.Pro332= (c.996T>C)?

DPH1 p.Pro332= (c.996T>C) is associated with developmental delay with short stature, dysmorphic facial features, and sparse hair (ClinVar).

Q: How common is DPH1 p.Pro332= (c.996T>C) in the general population?

DPH1 p.Pro332= (c.996T>C) is common (popmax 93.8%, eas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.996T>C · rs2236375 · VCV1182072

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Common

common (popmax 93.8%, eas) — too common for a highly-penetrant pathogenic allele

Conditions

developmental delay with short stature, dysmorphic facial features, and sparse hair

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -2.6	GERP -4.7
Overall
CADD	0.374	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 93.8% East Asian · 42,106/44,886 alleles

Filtering AF 93.1% ClinGen BA1/BS1 input FAF95, joint · FAF99 92.7%

Overall 77.8% 1,255,254/1,613,880 alleles · common

Ancestry group	Frequency	1 in
East Asiangrpmax	93.8%	1
Admixed American	87.3%	1
African / African-American	81.2%	1
Amishnot grpmax-eligible	80.8%	1
Ashkenazi Jewishnot grpmax-eligible	79.7%	1
Middle Eastern	79.5%	1
Remaining individualsnot grpmax-eligible	79%	1
Finnishnot grpmax-eligible	77.9%	1
European (non-Finnish)	76.9%	1
South Asian	70.9%	1

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: DPH1
Protein: p.Pro332=
Coding: c.996T>C
MANE Select: NM_001383
dbSNP: rs2236375
Type: single nucleotide variant
Location: chr17:2040594 (GRCh38)
Gene constraint: LOEUF 1.321 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.00

Full DPH1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

developmental delay with short stature, dysmorphic facial features, and sparse hair — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DPH1 p.Pro332Ala Uncertain significance ★ ⚠ same residue
DPH1 p.Leu229Pro Pathogenic/Likely pathogenic ★★ same condition
DPH1 p.Arg27His Uncertain significance ★★ ⚠ same condition
DPH1 p.Ile241Phe Uncertain significance ★★ same condition
DPH1 c.1228-21A>G Benign ★★ same condition
DPH1 c.400+117G>A Benign ★★ same condition
DPH1 p.Tyr128His Likely pathogenic ★ same condition
DPH1 p.Arg398His Uncertain significance ★ ⚠ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/dph1-p-pro332 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown