Is ELMOD2 p.Val39Gly (c.116T>G) pathogenic?

ELMOD2 p.Val39Gly (c.116T>G) is classified Likely benign in ELMOD2 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-11-11). AlphaMissense: likely benign (0.0861); Rare (popmax 0.341%, nfe).

How common is ELMOD2 p.Val39Gly (c.116T>G) in the general population?

ELMOD2 p.Val39Gly (c.116T>G) is rare (popmax 0.341%, nfe) (gnomAD).

What do computational predictors say about ELMOD2 p.Val39Gly (c.116T>G)?

AlphaMissense predicts likely benign (score 0.0861) — an in-silico prediction, not a clinical call.

ELMOD2 p.Val39Gly

c.116T>G · rs150922490 · VCV504726

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.0861 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.341%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0861	likely benign
REVEL	0.109	moderately benign-leaning
SaProt	LLR -6.84	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	Δ0.45	donor loss, 2 bp away · masked 0 · deltas
Constraint at this position
Conservation	phyloP 2.6	GERP 0.097, phastCons 1
Regional constraint	o/e 0.97	unconstrained · MANE · 25 kb · p 0.59 · regional, not allelic
Overall
CADD	18.31	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 0.341% European (non-Finnish) · 4,027/1,179,770 alleles

Filtering AF 0.332% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.329%

Overall 0.292% 4,708/1,613,336 alleles · rare

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.747%	134
European (non-Finnish)grpmax	0.341%	293
Remaining individualsnot grpmax-eligible	0.333%	300
Admixed American	0.274%	365
Middle Eastern	0.132%	757
African / African-American	0.0694%	1,442
Finnishnot grpmax-eligible	0.0437%	2,287

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: ELMOD2
Protein: p.Val39Gly
Coding: c.116T>G
MANE Select: NM_153702
dbSNP: rs150922490
Type: single nucleotide variant
Location: chr4:140525544 (GRCh38)
Gene constraint: LOEUF 0.881 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 94.39

Full ELMOD2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ELMOD2 c.142+43G>T Benign ★★ same type
ELMOD2 c.270-81T>G Benign ★★ same type
ELMOD2 c.-9-294A>G Benign ★★ same type
ELMOD2 c.*9C>T Benign/Likely benign ★★ same type
ELMOD2 p.Lys143Thr Benign/Likely benign ★★ same type
ELMOD2 p.Arg167Ser Uncertain significance ★ ⚠ same type
ELMOD2 p.Asn183Ile Uncertain significance ★ ⚠ same type
ELMOD2 p.Asn210Ser 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/elmod2-p-val39gly (accessed [today's date]).

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