Is RELT p.Ala314= (c.942C>T) pathogenic?

RELT p.Ala314= (c.942C>T) is classified Likely benign in RELT (ClinVar, No assertion criteria, 1 submitter; last evaluated 2020-01-20). Rare (popmax 0.27%, afr); Associated with RELT-related disorder.

What condition is associated with RELT p.Ala314= (c.942C>T)?

RELT p.Ala314= (c.942C>T) is associated with RELT-related disorder (ClinVar).

How common is RELT p.Ala314= (c.942C>T) in the general population?

RELT p.Ala314= (c.942C>T) is rare (popmax 0.27%, afr) (gnomAD).

RELT p.Ala314=

c.942C>T · rs149402638 · VCV3051926

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.27%, afr)

Conditions

RELT-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -0.78	GERP -4.4, phastCons 0.011
Overall
CADD	7.463	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.27% African / African-American · 203/75,064 alleles

Filtering AF 0.24% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.228%

Overall 0.0146% 235/1,613,720 alleles · rare exomes 121/1,461,372 · genomes 114/152,348 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.27%	370
Admixed American	0.02%	5,002
Remaining individualsnot grpmax-eligible	0.0192%	5,208
South Asian	0.00659%	15,182
European (non-Finnish)	0.000169%	590,012

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: RELT
Protein: p.Ala314=
Coding: c.942C>T
MANE Select: NM_152222
dbSNP: rs149402638
Type: single nucleotide variant
Location: chr11:73394630 (GRCh38)
Gene constraint: LOEUF 0.955 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 63.38

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

Disease context

RELT-related disorder

Similar variants

RELT p.Arg338Pro Likely benign same condition
RELT p.Met363Val Benign same condition
RELT p.Pro201= Benign same condition
RELT p.Thr256Met Benign same condition
RELT p.Thr360= Benign same condition
RELT p.Val367= Benign same condition
RELT p.Val367Glu Benign same condition
RELT p.Ala160= Likely benign ★★ 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/relt-p-ala314 (accessed [today's date]).

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