Is DTX1 p.Ser101= (c.303G>T) pathogenic?

DTX1 p.Ser101= (c.303G>T) is classified Benign in DTX1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2018-05-21). Common (popmax 10.4%, afr) — too common for a highly-penetrant pathogenic allele.

DTX1 p.Ser101=

Q: How common is DTX1 p.Ser101= (c.303G>T) in the general population?

DTX1 p.Ser101= (c.303G>T) is common (popmax 10.4%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.303G>T · rs116800762 · VCV768587

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Common

common (popmax 10.4%, afr) — too common for a highly-penetrant pathogenic allele

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 0.19	GERP -2.6, phastCons 0.9
Overall
CADD	6.993	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 10.4% African / African-American · 7,807/74,964 alleles

Filtering AF 10.2% ClinGen BA1/BS1 input FAF95, joint · FAF99 10.1%

Overall 0.576% 9,282/1,611,974 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	10.4%	10
Admixed American	0.814%	123
Remaining individualsnot grpmax-eligible	0.776%	129
Middle Eastern	0.512%	195
Ashkenazi Jewishnot grpmax-eligible	0.159%	629
European (non-Finnish)	0.0337%	2,964
South Asian	0.0286%	3,502
East Asian	0.00223%	44,854

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: DTX1
Protein: p.Ser101=
Coding: c.303G>T
MANE Select: NM_004416
dbSNP: rs116800762
Type: single nucleotide variant
Location: chr12:113077467 (GRCh38)
Gene constraint: LOEUF 0.74 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 76.10 · 5 PDB
Residue 101: the wwe 2 domain

Full DTX1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DTX1 p.Gly445Asp Uncertain significance ★★ ⚠ same type
DTX1 p.Ala226Glu Uncertain significance ★ ⚠ same type
DTX1 p.Ala226Thr Uncertain significance ★ ⚠ same type
DTX1 p.Ala256Ser Uncertain significance ★ ⚠ same type
DTX1 p.Ala260Val Uncertain significance ★ ⚠ same type
DTX1 p.Ala267Pro Uncertain significance ★ ⚠ same type
DTX1 p.Ala275Val Uncertain significance ★ ⚠ same type
DTX1 p.Ala307Val Uncertain significance ★ ⚠ same type

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/dtx1-p-ser101 (accessed [today's date]).

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