Is ELF1 p.Thr551Ile (c.1652C>T) pathogenic?

ELF1 p.Thr551Ile (c.1652C>T) is classified Uncertain significance in ELF1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-16). AlphaMissense: ambiguous (0.4616); Ultra-rare (popmax 0.0703%, sas).

How common is ELF1 p.Thr551Ile (c.1652C>T) in the general population?

ELF1 p.Thr551Ile (c.1652C>T) is ultra-rare (popmax 0.0703%, sas) (gnomAD).

What do computational predictors say about ELF1 p.Thr551Ile (c.1652C>T)?

AlphaMissense predicts ambiguous (score 0.4616) — an in-silico prediction, not a clinical call.

ELF1 p.Thr551Ile

c.1652C>T · rs150015002 · VCV2342134

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4616 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0703%, sas)

Computational evidence

Protein change
AlphaMissense	0.4616	ambiguous
REVEL	0.347	indeterminate
SaProt	LLR -10.14	damaging
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.9, phastCons 1
Overall
CADD	26.6	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 0.0703% South Asian · 64/91,088 alleles

Filtering AF 0.0564% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0514%

Overall 0.0201% 324/1,614,206 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0703%	1,423
Middle Eastern	0.033%	3,031
Admixed American	0.0317%	3,159
Ashkenazi Jewishnot grpmax-eligible	0.027%	3,701
Remaining individualsnot grpmax-eligible	0.024%	4,167
European (non-Finnish)	0.0181%	5,540
African / African-American	0.00266%	37,528
Finnishnot grpmax-eligible	0.00156%	64,036

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: ELF1
Protein: p.Thr551Ile
Coding: c.1652C>T
MANE Select: NM_032377 · reported on NM_172373
dbSNP: rs150015002
Type: single nucleotide variant
Location: chr13:40933633 (GRCh38)
Structure: AlphaFold pLDDT 85.98 · 7 PDB

Full ELF1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ELF1 p.Leu614= Benign ★★ same type
ELF1 p.Pro364= Benign ★★ same type
ELF1 p.Ala29Thr Uncertain significance ★ ⚠ same type
ELF1 p.Ala353Ser Uncertain significance ★ ⚠ same type
ELF1 p.Ala459Val Uncertain significance ★ ⚠ same type
ELF1 p.Arg323Thr Uncertain significance ★ ⚠ same type
ELF1 p.Arg328Gln Uncertain significance ★ ⚠ same type
ELF1 p.Arg330Lys 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/elf1-p-thr551ile (accessed [today's date]).

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