Is EOGT p.Pro24Arg (c.71C>G) pathogenic?

EOGT p.Pro24Arg (c.71C>G) is classified Benign/Likely benign in EOGT (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-01-27). AlphaMissense: likely benign (0.0673); Low-frequency (popmax 2.04%, sas); Associated with Adams-Oliver syndrome 4.

What condition is associated with EOGT p.Pro24Arg (c.71C>G)?

EOGT p.Pro24Arg (c.71C>G) is associated with Adams-Oliver syndrome 4 (ClinVar).

How common is EOGT p.Pro24Arg (c.71C>G) in the general population?

EOGT p.Pro24Arg (c.71C>G) is low-frequency (popmax 2.04%, sas) (gnomAD).

What do computational predictors say about EOGT p.Pro24Arg (c.71C>G)?

AlphaMissense predicts likely benign (score 0.0673) — an in-silico prediction, not a clinical call.

EOGT p.Pro24Arg

c.71C>G · rs140016031 · VCV784681

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.0673 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 2.04%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Adams-Oliver syndrome 4

Computational evidence

Protein change
AlphaMissense	0.0673	likely benign
REVEL	0.032	moderately benign-leaning
SaProt	LLR -5.94	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 1.6	GERP -0.99, phastCons 0.007
Regional constraint	o/e 1.10	unconstrained · MANE · 32 kb · p 0.016 · regional, not allelic
Overall
CADD	9.863	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 2.04% South Asian · 1,855/91,060 alleles

Filtering AF 1.96% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.93%

Overall 0.156% 2,521/1,614,054 alleles · low-frequency exomes 2,359/1,461,862 · genomes 162/152,192 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	2.04%	49
Ashkenazi Jewishnot grpmax-eligible	0.797%	125
Middle Eastern	0.346%	289
Remaining individualsnot grpmax-eligible	0.242%	414
Admixed American	0.0483%	2,069
European (non-Finnish)	0.0192%	5,221
African / African-American	0.004%	24,999

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: EOGT
Protein: p.Pro24Arg
Coding: c.71C>G
MANE Select: NM_001278689
dbSNP: rs140016031
Type: single nucleotide variant
Location: chr3:69009776 (GRCh38)
Gene constraint: LOEUF 1.121 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 91.71

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

Disease context

Adams-Oliver syndrome 4 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

EOGT c.1335-1G>A Pathogenic/Likely pathogenic ★★ same condition
EOGT c.311+1G>T Pathogenic/Likely pathogenic ★★ same condition
EOGT c.621-2A>T Pathogenic/Likely pathogenic ★★ same condition
EOGT p.Arg372Trp Uncertain significance ★★ ⚠ same condition
EOGT p.Arg377Trp Uncertain significance ★★ ⚠ same condition
EOGT p.Arg452His Uncertain significance ★★ ⚠ same condition
EOGT p.Arg470Trp Uncertain significance ★★ ⚠ same condition
EOGT p.Asp252Asn 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/eogt-p-pro24arg (accessed [today's date]).

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