Is CCL14 p.Val5Met (c.13G>A) pathogenic?

CCL14 p.Val5Met (c.13G>A) is classified Likely benign in CCL14 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-13). AlphaMissense: likely benign (0.0859); Very rare (popmax 0.00878%, sas).

How common is CCL14 p.Val5Met (c.13G>A) in the general population?

CCL14 p.Val5Met (c.13G>A) is very rare (popmax 0.00878%, sas) (gnomAD).

What do computational predictors say about CCL14 p.Val5Met (c.13G>A)?

AlphaMissense predicts likely benign (score 0.0859) — an in-silico prediction, not a clinical call.

CCL14 p.Val5Met

c.13G>A · rs779464556 · VCV3139710

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0859 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00878%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0859	likely benign
REVEL	0.005	strongly benign-leaning
SaProt	LLR -8.15	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 -8.6
Regional constraint	o/e 1.07	unconstrained · MANE · 2,845 bp · p 0.42 · regional, not allelic
Overall
CADD	0.024	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 0.00878% South Asian · 8/91,078 alleles

Filtering AF 0.00437% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00312%

Overall 0.00112% 18/1,613,708 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00878%	11,385
East Asian	0.00446%	22,443
Remaining individualsnot grpmax-eligible	0.0032%	31,237
Finnishnot grpmax-eligible	0.00313%	31,977
African / African-American	0.00267%	37,445
European (non-Finnish)	0.00017%	589,953

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: CCL14
Protein: p.Val5Met
Coding: c.13G>A
MANE Select: NM_032963
dbSNP: rs779464556
Type: single nucleotide variant
Location: chr17:35986637 (GRCh38)
Gene constraint: LOEUF 1.642 · pLI 0.04 (gnomAD)
Structure: AlphaFold pLDDT 86.15 · 2 PDB

Full CCL14 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

SCYL2 p.Leu478Pro Uncertain significance ★★ ⚠ same type
SCYL2 p.Met321Val Uncertain significance ★★ ⚠ same type
SCYL2 c.1096-23T>A Benign ★★ same type
SCYL2 c.177+35C>A Benign ★★ same type
SCYL2 p.Ile615Met Likely benign ★★ same type
SCYL2 p.Leu723= Benign ★★ same type
SCYL2 p.Arg100Ter Pathogenic ★ same type
SCYL2 p.Arg36Ter Pathogenic ★ 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/ccl14-p-val5met (accessed [today's date]).

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