Is ELOB p.Ala116Ser (c.346G>T) pathogenic?

ELOB p.Ala116Ser (c.346G>T) is classified Uncertain significance in ELOB (ClinVar, Single submitter, 1 submitter; last evaluated 2021-09-17). AlphaMissense: likely benign (0.1012); Very rare (popmax 0.00134%, afr).

How common is ELOB p.Ala116Ser (c.346G>T) in the general population?

ELOB p.Ala116Ser (c.346G>T) is very rare (popmax 0.00134%, afr) (gnomAD).

What do computational predictors say about ELOB p.Ala116Ser (c.346G>T)?

AlphaMissense predicts likely benign (score 0.1012) — an in-silico prediction, not a clinical call.

ELOB p.Ala116Ser

c.346G>T · rs1467138159 · VCV3088449

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1012 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00134%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1012	likely benign
REVEL	0.137	moderately benign-leaning
SaProt	LLR -6.17	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 1.7, phastCons 1
Regional constraint	o/e 0.79	unconstrained · MANE · 5,246 bp · p 0.0086 · regional, not allelic
Overall
CADD	22.7	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00134% African / African-American · 1/74,780 alleles

Overall 0.000658% 1/152,062 alleles · very rare

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: ELOB
Protein: p.Ala116Ser
Coding: c.346G>T
MANE Select: NM_007108
dbSNP: rs1467138159
Type: single nucleotide variant
Location: chr16:2772001 (GRCh38)
Gene constraint: LOEUF 0.788 · pLI 0.62 (gnomAD)
Structure: AlphaFold pLDDT 93.01 · 231 PDB
Residue 116: the 'disordered' region

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

Similar variants

ELOB c.*397A>G Uncertain significance ★ same type
ELOB c.*402C>A Uncertain significance ★ same type
ELOB c.*405A>G Uncertain significance ★ same type
ELOB c.*406C>T Uncertain significance ★ same type
ELOB c.*408A>G Uncertain significance ★ same type
ELOB c.*412C>T Uncertain significance ★ same type
ELOB c.*427C>A Uncertain significance ★ same type
ELOB c.*447G>C 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/elob-p-ala116ser (accessed [today's date]).

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