Is ELOVL5 p.Cys61= (c.183C>T) pathogenic?

ELOVL5 p.Cys61= (c.183C>T) is classified Likely benign in ELOVL5 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-03-02). Very rare (popmax 0.00659%, sas).

How common is ELOVL5 p.Cys61= (c.183C>T) in the general population?

ELOVL5 p.Cys61= (c.183C>T) is very rare (popmax 0.00659%, sas) (gnomAD).

ELOVL5 p.Cys61=

c.183C>T · VCV4847594

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00659%, sas)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6	GERP 0.99, phastCons 1
Overall
CADD	9.862	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00659% South Asian · 6/91,074 alleles

Filtering AF 0.00286% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00195%

Overall 0.000684% 10/1,461,728 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00659%	15,179
Remaining individualsnot grpmax-eligible	0.0048%	20,833
European (non-Finnish)	8.48e-05%	1,179,933

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: ELOVL5
Protein: p.Cys61=
Coding: c.183C>T
MANE Select: NM_021814
Type: single nucleotide variant
Location: chr6:53291839 (GRCh38)
Gene constraint: LOEUF 0.405 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 82.53

Full ELOVL5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ELOVL5 p.Ala102Thr Uncertain significance ★★ ⚠ same type
ELOVL5 p.Arg111His Uncertain significance ★★ ⚠ same type
ELOVL5 p.Arg193Cys Uncertain significance ★★ ⚠ same type
ELOVL5 p.Arg62Gln Uncertain significance ★★ ⚠ same type
ELOVL5 p.Asp268Gly Uncertain significance ★★ ⚠ same type
ELOVL5 p.His3Arg Uncertain significance ★★ ⚠ same type
ELOVL5 p.Ile109Leu Uncertain significance ★★ ⚠ same type
ELOVL5 p.Ile33Leu 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/elovl5-p-cys61 (accessed [today's date]).

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